Combine ICF scores in a pairwise manner.
combineInteractionChangedFeats(
icfObject,
selected_ints = NULL,
selected_feats = NULL,
specific_feats_1 = NULL,
specific_feats_2 = NULL,
min_cells = 5,
min_int_cells = 3,
min_fdr = 0.05,
min_spat_diff = 0,
min_log2_fc = 0.5,
do_parallel = TRUE,
verbose = TRUE
)
combineICF(
icfObject,
selected_ints = NULL,
selected_feats = NULL,
specific_feats_1 = NULL,
specific_feats_2 = NULL,
min_cells = 5,
min_int_cells = 3,
min_fdr = 0.05,
min_spat_diff = 0,
min_log2_fc = 0.5,
do_parallel = TRUE,
verbose = TRUE
)
ICF (interaction changed feat) score object
subset of selected cell-cell interactions (optional)
subset of selected Features (optional)
specific Featureset combo (need to position match specific_feats_2)
specific Featureset combo (need to position match specific_feats_1)
minimum number of target cell type
minimum number of interacting cell type
minimum adjusted p-value
minimum absolute spatial expression difference
minimum absolute log2 fold-change
run calculations in parallel with mclapply
verbose
`combIcfObject` that contains the filtered differential feature scores
g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> python already initialized in this session
#> active environment : '/usr/bin/python3'
#> python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#> "/usr/bin/python3"
g_icf <- findInteractionChangedFeats(g,
cluster_column = "leiden_clus",
selected_feats = c("Gna12", "Ccnd2", "Btbd17"),
nr_permutations = 10
)
#> Error: package 'future' is not yet installed
#>
#> To install:
#> install.packages(c("future"))
cicf <- combineInteractionChangedFeats(g_icf)
#> Error: object 'g_icf' not found
force(cicf)
#> Error: object 'cicf' not found
combineICF(g_icf) # this is a shortened alias
#> Error: object 'g_icf' not found